IndexError: list index out of range

[aparnasing]

Hi, I am using idr to process 2 replicate bed files but getting an index error. copying command and bash response
idr --samples dyadvscolrep1_c3.0_common.bed dyadvscolrep2_c3.0_common.bed
/usr/local/bin/idr --samples dyadvscolrep1_c3.0_common.bed dyadvscolrep2_c3.0_common.bed
Traceback (most recent call last):
File "/usr/local/bin/idr", line 4, in
import('pkg_resources').run_script('idr==2.0.3', 'idr')
File "/usr/local/lib/python3.6/site-packages/pkg_resources/init.py", line 743, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/usr/local/lib/python3.6/site-packages/pkg_resources/init.py", line 1498, in run_script
exec(code, namespace, namespace)
File "/usr/local/lib/python3.6/site-packages/idr-2.0.3-py3.6-linux-x86_64.egg/EGG-INFO/scripts/idr", line 10, in
idr.idr.main()
File "/usr/local/lib/python3.6/site-packages/idr-2.0.3-py3.6-linux-x86_64.egg/idr/idr.py", line 839, in main
merged_peaks, signal_type = load_samples(args)
File "/usr/local/lib/python3.6/site-packages/idr-2.0.3-py3.6-linux-x86_64.egg/idr/idr.py", line 703, in load_samples
for fp in args.samples]
File "/usr/local/lib/python3.6/site-packages/idr-2.0.3-py3.6-linux-x86_64.egg/idr/idr.py", line 703, in
for fp in args.samples]
File "/usr/local/lib/python3.6/site-packages/idr-2.0.3-py3.6-linux-x86_64.egg/idr/idr.py", line 53, in load_bed
signal = float(data[signal_index])
IndexError: list index out of range

[melnuesch]

I got a similar error. Any thoughts?

Traceback (most recent call last):
File "/Users/nueschm/miniconda3/bin/idr", line 4, in
import('pkg_resources').run_script('idr==2.0.2', 'idr')
File "/Users/nueschm/miniconda3/lib/python3.7/site-packages/pkg_resources/init.py", line 666, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/Users/nueschm/miniconda3/lib/python3.7/site-packages/pkg_resources/init.py", line 1453, in run_script
exec(code, namespace, namespace)
File "/Users/nueschm/miniconda3/lib/python3.7/site-packages/idr-2.0.2-py3.7-macosx-10.7-x86_64.egg/EGG-INFO/scripts/idr", line 10, in
idr.idr.main()
File "/Users/nueschm/miniconda3/lib/python3.7/site-packages/idr-2.0.2-py3.7-macosx-10.7-x86_64.egg/idr/idr.py", line 733, in main
merged_peaks, signal_type = load_samples(args)
File "/Users/nueschm/miniconda3/lib/python3.7/site-packages/idr-2.0.2-py3.7-macosx-10.7-x86_64.egg/idr/idr.py", line 620, in load_samples
for fp in args.samples]
File "/Users/nueschm/miniconda3/lib/python3.7/site-packages/idr-2.0.2-py3.7-macosx-10.7-x86_64.egg/idr/idr.py", line 620, in
for fp in args.samples]
File "/Users/nueschm/miniconda3/lib/python3.7/site-packages/idr-2.0.2-py3.7-macosx-10.7-x86_64.egg/idr/idr.py", line 39, in load_bed
if peak_summit_index == None or int(data[peak_summit_index]) == -1:
IndexError: list index out of range

[hjames1]

I got a similar error,too.

Traceback (most recent call last):
File "/home/u100395/workdir/miniconda3/envs/chipseq/bin/idr", line 10, in
idr.idr.main()
File "/home/u100395/workdir/miniconda3/envs/chipseq/lib/python3.7/site-packages/idr/idr.py", line 840, in main
merged_peaks, signal_type = load_samples(args)
File "/home/u100395/workdir/miniconda3/envs/chipseq/lib/python3.7/site-packages/idr/idr.py", line 732, in load_samples
f1, f2 = [load_bed(fp, signal_index) for fp in args.samples]
File "/home/u100395/workdir/miniconda3/envs/chipseq/lib/python3.7/site-packages/idr/idr.py", line 732, in
f1, f2 = [load_bed(fp, signal_index) for fp in args.samples]
File "/home/u100395/workdir/miniconda3/envs/chipseq/lib/python3.7/site-packages/idr/idr.py", line 65, in load_bed
float(data[6]), float(data[7]), float(data[8])
IndexError: list index out of range

[yx-xu]

Hello!
I got an error same to this, but I couldn't resolve it. Have you solved the problem? Could you help me about this? Thank you very much!
Looking forward to your reply!

[karl1926]

I had a similar issue. Any news?

[Suger0917]

I had a similar error.
File "/storage/xx/software/miniconda3/lib/python3.9/site-packages/idr-2.0.2-py3.9-linux-x86_64.egg/idr/idr.py", line 45, in load_bed
peak = Peak(data[0], data[5],
IndexError: list index out of range
File "/storage/xx/software/miniconda3/lib/python3.9/site-packages/idr-2.0.2-py3.9-linux-x86_64.egg/idr/idr.py", line 45, in load_bed
peak = Peak(data[0], data[5],
IndexError: list index out of range

Peak score is in the column 5th. In python, actual index is equal to py_index+1. So I set peak = Peak(data[0], data[4] in line 45 of idr.py. This error disappeared.

[brottodb]

I am having a similar problem. Anyone was able to solve this issue? Thanks!

[luorongxin-yuan]

had similar problem at line 65 when my input bed file is 8 columns, but 9 is expected. So I just kept the original 6 columns, and filled column 7-9 with 0s. Seemed to solve the problem, hopefully not interfering with statistics
File "/home/u100395/workdir/miniconda3/envs/chipseq/lib/python3.7/site-packages/idr/idr.py", line 65, in load_bed
float(data[6]), float(data[7]), float(data[8])
IndexError: list index out of range